Over the past few weeks it appears two spots in almost identical spots on either side of my back plate have developed rust or bubbling. There is no recall for my car and it's weird that this would happen in similar spots so close in time.

1. Is this something I can repair by myself by buying a specific charcoal beige aerosol paint can? 2. Can a body shop get the same color as my car and paint these two small areas? 3. Or is a body shop going to have to paint the whole panel of my trunk?

This is not a thing to attempt to fix on your own, it will look horrible if you try to spray paint it

They will have to remove that plastic molding and fix the affected area.. It's probably rusted a little under the plastic moulding (welcome to canada).. Depending on the bodyshop they might re-paint the whole trunk lid or blend in new paint.. Get a few quotes and see what they it will cost.